In a significant development, the Maharashtra government will conduct a parallel investigation into the Elgar Parishad-Koregaon-Bhima case, a senior state minister said here on Monday.

"We shall seek legal opinion in the matter. We shall also discuss the matter with the Chief Minister before setting up a Special Investigation Team," Home Minister Anil Deshmukh said.

Earlier Nationalist Congress Party national spokesperson and Minority Affairs Minister Nawab Malik had said that the state government will set up a SIT to probe the sensitive case soon.

A decision on this will be taken soon by Deshmukh, he added, four days after a Pune Sessions Court assigned the case to the National Investigation Agency (NIA).

The move came a day after NCP President Sharad Pawar alleged that the Centre had handed over the case to the NIA as the previous Bharatiya Janata Party government in the state "wants to hide something".

"There appears to be something that the former (Devendra) Fadnavis government wants to suppress. That's why the probe has been handed over to the NIA. The Fadnavis government was in power when the Koregaon-Bhima violence broke out," Pawar told media persons in Jalgaon on Sunday.

Earlier, on at least two occasions, Pawar had taken a swipe at Chief Minister Uddhav Thackeray saying it was "improper" to hand over the case to NIA, but the Sena has not yet reacted.

However, Pawar had also said the CM was within rights to use his discretionary powers and it was the Centre's prerogative to investigate the matter, "but the Maha Vikas Aghadi government should have been taken into confidence".

The Elgar Parishad-Koregaon-Bhima case has been a bone of contention between the Centre and Maharashtra besides creating a huge friction between ruling allies - the Shiv Sena and the NCP-Congress - since the past three weeks.

The row started after Pawar shot off a letter to the state government last month, demanding a separate probe into the role of the Pune police which had investigated the matter, and barely a couple of days after that, the Centre ordered the NIA to take over the case.